I'm just going through the game again with the commentary on, too. When I noticed the 14A number in his phone I thought to myself "Mm-mmm, that's good foreshadowing". I noticed Ed hang his head after talking to Morales on the phone the first time through, I thought it was interesting but then soon forgot about it. Seeing it now, it all makes sense and is a really subtle yet very poignant thing that they put in there. And the tragic irony of Anna dropping the coin. It's her lucky coin and she thinks of it as something that always helps her, yet if she hadn't dropped it at that moment, Ed couldn't have ingratiated himself with her and she wouldn't have ended up like she did. Oh, and Ed leaving the subway in what I think is the graveyard where Anna's family are buried.
Though one thing I don't really get that I only saw this playthrough; if you make Bennet enter the post office, he gets shot. But why? Why would Amul shoot him? It maybe makes sense on the first playthrough since this is "criminals" doing "bad things", so they might shoot a nosey cop. But when you know what they're doing, and how they actually want Bennet and co. to work together (and when Reno should be able to predict this kind of stuff) it makes no sense at all that they'd kill Bennet.